R Observatory: Metrics for POINT version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

POINT

1.4

Protein Structure Guided Local Test

0packages depend

6.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Shannon T. HollowayFirst published 2019-03-054 releasesCRAN page ↗

Provides an implementation of a rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level. For details of the implemented method see West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S-M., Wagner M. J., Buse, J. B., Motsinger-Reif, A., Fourches, D., and Tzeng, J-Y. (2019) doi:10.1371/journal.pcbi.1006722.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("POINT", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-point

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-POINT

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-POINT

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6.5K

CRAN downloads in the past year

Rank #7,525 · ~18/day · ~539/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

1.2K90 days

6.5K1 year

Compare downloads with other packages →

Also on101 r2u8 autocran

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (5)

methodsstatsrARPACKMatrixCompQuadForm

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Shannon T. Holloway

Author, Maintainer

Authors (2)

Shannon T. Holloway

Author, Maintainer

Rachel Marceau West

Author

Listed in earlier versions (2)

Holloway

no longer listed · 1.4

West

no longer listed · 1.4

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.4Latest
2025-05-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3
2023-10-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1
2019-03-05
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-05
Total releases: 4 / 7 yrs
License: GPL-2 OSI
Download size: 11 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("POINT")

Format

Holloway, S. T., & West, R. M. (2025). POINT: Protein Structure Guided Local Test (Version 1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.POINT

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for POINT version 1.4 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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